check_class_col

A table, list, or vector that contain sequence IDs, taxon
IDs, or taxon names.<ul>
<li>tables: The <code>column</code> option must be used to specify which column
contains the sequence IDs, taxon IDs, or taxon names.</li>
<li>lists: There must be only one item per list entry unless the <code>column</code>
option is used to specify what item to use in each list entry.</li>
<li>vectors: simply a vector of sequence IDs, taxon IDs, or taxon names.</li>
</ul>

tax_data

(<code>character</code> or <code>integer</code>) The name or index of the column that
contains information used to lookup classifications. This only applies when
a table or list is supplied to <code>tax_data</code>.

column

Used by parse_tax_data and lookup_tax_data to check that columm/class_col is valid for the input data

internal

Provides taxonomic classes for
groupings of taxonomic names without data, and those
with data. Methods provided are "taxonomically aware", in
that they know about ordering of ranks, and methods that
filter based on taxonomy also filter associated data.
This package is described in the publication: "Taxa: An R
package implementing data standards and methods for
taxonomic data", Zachary S.L. Foster, Scott Chamberlain,
Niklaus J. Gr<c3><bc>nwald (2018) <doi:10.12688/f1000research.14013.2>.

check_class_col: Check for name/index in input data

Description

Usage

Arguments